Extended Data Fig. 4: Soft thresholding power determination for WGCNA and module and trait clustering of the WGCNA network. | Nature Microbiology

Extended Data Fig. 4: Soft thresholding power determination for WGCNA and module and trait clustering of the WGCNA network.

From: Co-expression analysis reveals distinct alliances around two carbon fixation pathways in hydrothermal vent symbionts

Extended Data Fig. 4: Soft thresholding power determination for WGCNA and module and trait clustering of the WGCNA network.

a, The scale free fit index for soft thresholding powers. b, Mean connectivity as a function of soft thresholding powers. c, Scale free topology of frequency distribution of connectivity p(k) when the soft thresholding power is β = 8. d, Histogram of mean connectivity when the soft thresholding power is β = 8. e, Gene dendrogram with colors along the bottom indicating module color assignment using hierarchical clustering based on TOM dissimilarity (top color row). Bottom color row is module assignment after using a dynamic splicing method, merging highly connected modules with branches reaching below 0.3. f, Sample dendrogram and trait heatmap. The leaves of the tree correspond to samples from individual Riftia. Red color bands correspond to aquaria conditions in aquaria listed on left (for aquaria conditions and abbreviation key see Fig.1 and Supplementary Table 1). Bottom rows represent conditions merged according to substrate represented by sulfide, hydrogen, oxygen and nitrate. The last row indicates the year these experiments occurred (red represents 2014, white represents 2016).

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